Variant report

Variant	rs3788492
Chromosome Location	chr22:33128761-33128762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11089592	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1894453	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1894454	0.92[ASN][1000 genomes]
rs2008206	0.89[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2157138	0.93[ASN][1000 genomes]
rs2413145	0.91[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2413146	0.95[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2413147	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3788487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788489	0.89[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3788490	0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3788491	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3788493	0.87[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3788494	0.88[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3788495	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3788496	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs3788497	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs3827340	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4821091	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5754240	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs5994613	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5998601	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5998605	0.95[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs5998607	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs743739	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs762885	0.89[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9606988	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064719	chr22:33028891-33159636	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv588897	chr22:33116314-33139230	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3788492	XBP1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33120000-33129600	Weak transcription	Right Atrium	heart
2	chr22:33121800-33141400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr22:33127800-33133000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr22:33127800-33133200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr22:33128000-33130400	Weak transcription	Spleen	Spleen
6	chr22:33128200-33129600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr22:33128400-33132200	Enhancers	Thymus	Thymus
8	chr22:33128400-33135000	Enhancers	Fetal Thymus	thymus

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